Projects in winter semester 2025/26

Accelerate indexing with ray-tracing RTX GPU cores

Slots: 2, Hours per week: 4, Completion within: 9 months
For students inrolled in: Informatics B.Ed., Informatics B.Sc., Mathematics-Infomatics B.Sc., Physics B.Sc.,

Discription
The project aims to accelerate indexing processes of GPU databanks with the help of cutting-edge ray tracing. It also aims to search data structures quickly and quantify properties. Ray tracing uses an internal hardware-accelerated data structure where details remain unknown. The project aims to investigate this ray-tracing process.
Role of the students
The students will use ready-made Python code to analyze potential physical effects and applications of such friction between rotating particles in computer simulations. If they are interested, students can also adjust the source code.
Qualifications
Previous knowledge of programming languages and GPUs is required.
(more information)

The influence of rotational friction between particles

Slots: 1-4, Hours per week: 3-9, Completion within: 3-12 months
For students inrolled in: Applied Physics B.Sc., Informatics B.Ed., Informatics B.Sc., Mathematics B.Ed., Mathematics B.Sc., Meteorology B.Sc., Physics B.Ed., Physics B.Sc.,

Discription
Friction between rotating particles plays a key role in various physical or biological contexts and is under investigation in an SFB (Sonderforschungsbereich) in Mainz. Such particles like bacteria, for example, can be used as motors for bacteria-based batteries. This project will explore the influence of rotational friction between particles in typical molecular dynamic simulations.
Role of the students
The students will use ready-made Python code to analyze potential physical effects and applications of such friction between rotating particles in computer simulations. If they are interested, students can also adjust the source code.
Qualifications
Basic Python skills are necessary. You will have to use Linux in this project. However, you won't need basic Linux skills since you will learn it through the project.
(more information)

Setting up Molecular Dynamic Simulations to determine Binding sites on MoHik1p

Slots: 1, Hours per week: 4, Completion within: 9 months
For students inrolled in: Biology B.Sc., BMC B.Sc., Chemestry B.Sc., Mathematics-Infomatics B.Sc., Molecular Biology B.Sc., Molecular Biotechnology B.Sc., Physics B.Sc.,

Discription
MoHik1p is a protein that is crucial for the mechanism of action of Fludioxonil which is a common fungicide. But its exact mechanism is still unclear and we want to use MD simulations to get deeper insights to the protein - ligand interactions.
Role of the students
Your task will be to set up MD simulations, learn the basic concepts of simulation methods, and interpret the results. The simulations will be performed using the common Gromacs simulation software, while the analysis will be performed in VMD and using Python modules like MDAnalysis.
Qualifications
Basic Python and MD simulation skills are necessary. You will have to use Linux in this project. However, you won't need basic Linux skills since you will learn it through the project.
(more information)

Toolchain for the statistical evaluation of runtimes of various algorithms in the HPC area

Slots: 1, Hours per week: 3-9, Completion within: 3-12 months
For students inrolled in: Informatics B.Ed., Informatics B.Sc., Mathematics-Infomatics B.Sc.,

Discription
Goal of the project is to develop and test a toolchain for the statistical evaluation of runtimes of various algorithms in the HPC area.
Role of the students
The student will develop said toolchain under the guidance of the supervisor.
Qualifications
Basic Python skills are necessary. Most texts will be in English which is why the student should have some English reading skills.
(more information)

The feeling of relevance for mathematical contents in science degree programms

Slots: 1, Hours per week: 3, Completion within: 9 months
For students inrolled in: Mathematics B.Ed., Mathematics B.Sc., Mathematics-Infomatics B.Sc.,

Discription
The lack of perceived relevance of mathematical content in science degree programs is often cited in the literature as a possible reason for dropping out of university. The investigation of reasons and motivations for increasing this perception of relevance and the identification of successful strategies is the aim our research project. In the course of the QUEST project, initial strategies and their effect are to be investigated using the Fundamentals of Numerics course with the help of new tasks and application examples. In particular, the relevance of the course for the future profession for Mathematics B. Ed. and B.Sc. will be addressed.
Role of the students
The task is to carry out and analyze an evaluation of the perceived relevance.
Qualifications
Basic knowledge of programming is helpful, but not essential.
(more information)

Projects in summer semester 2025

Phase Behavior and Morphological Analysis of 2D Colloidal Monolayers

Slots: 2, Hours per week: 6, Completion within: 6 months
For students inrolled in: Applied Physics B.Sc., Environmental Sciences with a Focus in Atmosphere and Climate B.Sc., Informatics B.Ed., Informatics B.Sc., Mathematics B.Ed., Mathematics B.Sc., Mathematics-Infomatics B.Sc., Meteorology B.Sc., Physics B.Ed., Physics B.Sc.,

Discription
Two-dimensional self-assembled colloidal particle monolayers have wide-ranging applications in nanotechnology. The phase behavior of such monolayers is predominantly influenced by inter-particle interactions. For example, in a 2D monolayer, an increase in particle diameter can induce phase transitions from a liquid-like state to a hexatic phase and ultimately to a crystalline solid phase. This project aims to give students basic understanding of the physics governing the self-assembly process and to provide hands-on experience with advanced tools for analyzing the morphology of two-dimensional colloidal assemblies.
Role of the students
The student will perform particle-based simulations using molecular dynamics (MD) software to explore the morphology of self-assembled structures by tuning inter-particle interactions. They will study the physics of self-assembly and analyze phase morphology using techniques such as 2D Fourier transforms, Delaunay triangulation, order parameters, and correlation functions.
Qualifications
The ideal candidate is motivated, enthusiastic, and committed to learning new tools and techniques. A basic knowledge of programming languages such as Python or C/C++ is essential. Preference will be given to students with a background in physics, mathematics, or computational physics. Proficiency in English is required for communication.
(more information)

Multi-scale biomolecular simulations - analysis of protein interaction patterns

Slots: 1, Hours per week: 4, Completion within: 9 months
For students inrolled in: Applied Physics B.Sc., BMC B.Sc., Chemestry B.Sc., Informatics B.Ed., Informatics B.Sc., Mathematics B.Ed., Mathematics B.Sc., Mathematics-Infomatics B.Sc., Physics B.Ed., Physics B.Sc.,

Discription
In collaboration with our experimental partner at IMB, we study protein granules, a molecular condensate involved in epigenetic inheritance. To study their formation, we use molecular dynamics simulations and analyze protein interaction patterns. These help us investigate the underlying biophysical mechanism.
Role of the students
This QUEST project offers a first perspective on biophysical research on proteins that play a role in epigenetic inheritance. We perform molecular dynamics (MD) simulations on MOGON2, extracting insights by analyzing contact patterns. You can choose your focus to work with us on advancing our Python workflow: (a) pattern analysis through frequent item set mining or simple ML/generative models, (b) performance optimization via benchmarking and test development, or (c) molecular system exploration through sequence mutations.
Qualifications
Curiosity to support protein research through simulations and method development is helpful. You should be interested in collaborating with a PhD student in an interdisciplinary lab. A first experience with Python is helpful or at least you should bring high motivation to develop programming skills. Some interest in gaining experience with High-Performance Computing (HPC) systems is recommended.
(more information)

Creating an analysis framework for Coarse-Grained LLPS-Simulations

Slots: 1, Hours per week: 6, Completion within: 6 months
For students inrolled in: Applied Physics B.Sc., BMC B.Sc., Chemestry B.Ed., Chemestry B.Sc., Environmental Sciences with a Focus in Atmosphere and Climate B.Sc., Geography B.Ed., Geography B.Sc., Geosciences B.Sc., Informatics B.Ed., Informatics B.Sc., Mathematics B.Ed., Mathematics B.Sc., Mathematics-Infomatics B.Sc., Meteorology B.Sc., Molecular Biology B.Sc., Molecular Biotechnology B.Sc., Physics B.Ed., Physics B.Sc.,

Discription
Complementary to the work of our experimentalists in biology, we investigate the liquid-liquid phase separation (LLPS) of different proteins using coarse-grained molecular dynamics (MD) simulations. To create a phase diagram, many simulations with varying starting parameters are carried out and evaluated according to the same scheme. Additional features are to be added to the existing framework for this purpose.
Role of the students
The students implement new analysis features and thus gain an insight into research using biophysical simulations, as well as the development of research software using test-driven development.
Qualifications
Basic knowledge of statistical physics, programming and willingness to familiarize yourself with an interdisciplinary field are required. Knowledge of MD simulations, the Julia programming language, good English skills, Git and statistics are advantageous.
(more information)

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